1
|
Szabo R, Nagy C, Gaspar A. Direct Injection Electrospray Ionization Mass Spectrometry (ESI-MS) Analysis of Proteins with High Matrix Content:Utilizing Taylor-Aris Dispersion. Angew Chem Int Ed Engl 2024; 63:e202318225. [PMID: 38294363 DOI: 10.1002/anie.202318225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/27/2024] [Accepted: 01/29/2024] [Indexed: 02/01/2024]
Abstract
This is the first work demonstrating the utility of the Taylor-Aris (TA) dispersion in avoiding serious interference issues commonly occurring in the electrospray ionization-mass spectrometric (ESI-MS) determination of therapeutic protein pharmaceuticals undergoing no pre-separation or sample purification. It was also pointed out that the TA dispersion conditions and its analytical utilization for proteomics can be easily accomplished in a commercial CE-MS instrument. In the proposed Taylor-Aris dispersion-assisted mass spectrometry (TADA-MS) analysis 0.5 μL sample is injected into a 65 cm long 50 μm i.d. capillary and pumped with 1 bar toward the MS. The procedure is efficient for the direct injection analysis of components having low diffusion coefficients (proteins) that are present in complex matrices of small organic and inorganic compounds.
Collapse
Affiliation(s)
- Ruben Szabo
- Department of Inorganic and Analytical Chemistry, Institute of Chemistry, University of Debrecen, Debrecen, 4032, Hungary
| | - Cynthia Nagy
- Department of Inorganic and Analytical Chemistry, Institute of Chemistry, University of Debrecen, Debrecen, 4032, Hungary
| | - Attila Gaspar
- Department of Inorganic and Analytical Chemistry, Institute of Chemistry, University of Debrecen, Debrecen, 4032, Hungary
| |
Collapse
|
2
|
Yang Y, Yang Y, Wang S, Li H, Chen DDY. Detecting the formation of human c-KIT oncogene promoter G-Quadruplex by Taylor dispersion analysis. Talanta 2021; 233:122533. [PMID: 34215036 DOI: 10.1016/j.talanta.2021.122533] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 05/14/2021] [Accepted: 05/15/2021] [Indexed: 11/16/2022]
Abstract
The formation of G-quadruplex (G4) structures in oncogenic G-rich promoter regions are implicated in their biological functions, especially the inhibition of transcription. The binding of cations is thought to contribute to the stabilization of the G4 formation and competition against the duplex formation in the genomic sequence. Furthermore, it might affect the recognition of DNA-binding proteins. Therefore, measuring the interaction between G4 DNA and cations in a free solution environment is critical for evaluating G4 DNA biological functions. However, how binding to cations (K+ and NH4+) affects the folding equilibrium of the G4 structure remains unclear. In this work, a Taylor dispersion analysis (TDA) method using a capillary electrophoresis (CE) instrument was established for the quantitative characterization of the cation-dependent G4 formation in the human c-KIT oncogene promoter region, as well as diffusivities and hydrodynamic radii of DNA variations before and after folding. Our results showed that both K+ and NH4+ can induce the random-coiled c-KIT DNA to unfold and form a more unstretched intermediate state and then fold into tightly structured G4s with smaller size. The G4 size induced by NH4+ was smaller than that induced by K+ ions, though these two cations induced the c-KIT G4 DNA formation with similar binding constants (order of magnitude around 106 M-1). The TDA method can be widely used for rapid structural analyses of trace amounts of DNA mixtures, which effectively differentiate DNA variations or DNA-ligand complex conformations.
Collapse
Affiliation(s)
- Yunhe Yang
- National and Local Joint Engineering Research Center of Biomedical Functional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Changzhou Institute of Innovation and Development, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, PR China
| | - Yang Yang
- National and Local Joint Engineering Research Center of Biomedical Functional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Changzhou Institute of Innovation and Development, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, PR China
| | - Shuangshuang Wang
- National and Local Joint Engineering Research Center of Biomedical Functional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Changzhou Institute of Innovation and Development, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, PR China
| | - Huihui Li
- National and Local Joint Engineering Research Center of Biomedical Functional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Changzhou Institute of Innovation and Development, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, PR China.
| | - David D Y Chen
- Department of Chemistry, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
| |
Collapse
|
3
|
Hong J, Wu H, Zhang R, He M, Xu W. The Coupling of Taylor Dispersion Analysis and Mass Spectrometry to Differentiate Protein Conformations. Anal Chem 2020; 92:5200-5206. [DOI: 10.1021/acs.analchem.9b05745] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jie Hong
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Haimei Wu
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Rongkai Zhang
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Muyi He
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
- Institute of Food Safety, Chinese Academy of Inspection & Quarantine, Beijing 100176, China
| | - Wei Xu
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| |
Collapse
|
4
|
Zuk PJ, Cichocki B, Szymczak P. GRPY: An Accurate Bead Method for Calculation of Hydrodynamic Properties of Rigid Biomacromolecules. Biophys J 2018; 115:782-800. [PMID: 30144937 PMCID: PMC6127458 DOI: 10.1016/j.bpj.2018.07.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 07/08/2018] [Accepted: 07/16/2018] [Indexed: 10/28/2022] Open
Abstract
Two main problems that arise in the context of hydrodynamic bead modeling are an inaccurate treatment of bead overlaps and the necessity of using volume corrections when calculating intrinsic viscosity. We present a formalism based on the generalized Rotne-Prager-Yamakawa approximation that successfully addresses both of these issues. The generalized Rotne-Prager-Yamakawa method is shown to be highly effective for the calculation of transport properties of rigid biomolecules represented as assemblies of spherical beads of different sizes, both overlapping and nonoverlapping. We test the method on simple molecular shapes as well as real protein structures and compare its performance with other computational approaches.
Collapse
Affiliation(s)
- Pawel J Zuk
- Department of Biosystems and Soft Matter, Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw, Poland; Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, New Jersey
| | - Bogdan Cichocki
- Institute of Theoretical Physics, Faculty of Physics, University of Warsaw, Warsaw, Poland
| | - Piotr Szymczak
- Institute of Theoretical Physics, Faculty of Physics, University of Warsaw, Warsaw, Poland.
| |
Collapse
|
5
|
Quantitative correlations between collision induced dissociation mass spectrometry coupled with electrospray ionization or atmospheric pressure chemical ionization mass spectrometry – Experiment and theory. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2017.12.098] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
|
6
|
Fleming PJ, Fleming KG. HullRad: Fast Calculations of Folded and Disordered Protein and Nucleic Acid Hydrodynamic Properties. Biophys J 2018; 114:856-869. [PMID: 29490246 PMCID: PMC5984988 DOI: 10.1016/j.bpj.2018.01.002] [Citation(s) in RCA: 106] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 12/28/2017] [Accepted: 01/02/2018] [Indexed: 11/16/2022] Open
Abstract
Hydrodynamic properties are useful parameters for estimating the size and shape of proteins and nucleic acids in solution. The calculation of such properties from structural models informs on the solution properties of these molecules and complements corresponding structural studies. Here we report, to our knowledge, a new method to accurately predict the hydrodynamic properties of molecular structures. This method uses a convex hull model to estimate the hydrodynamic volume of the molecule and is orders of magnitude faster than common methods. It works well for both folded proteins and ensembles of conformationally heterogeneous proteins and for nucleic acids. Because of its simplicity and speed, the method should be useful for the modification of computer-generated, intrinsically disordered protein ensembles and ensembles of flexible, but folded, molecules in which rapid calculation of experimental parameters is needed. The convex hull method is implemented in a Python script called HullRad. The use of the method is facilitated by a web server and the code is freely available for batch applications.
Collapse
Affiliation(s)
- Patrick J Fleming
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland
| | - Karen G Fleming
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland.
| |
Collapse
|
7
|
Hahn DK, Aragon SR. Intrinsic Viscosity of Proteins and Platonic Solids by Boundary Element Methods. J Chem Theory Comput 2015; 2:1416-28. [PMID: 26626849 DOI: 10.1021/ct600062y] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The boundary element (BE) method is used to implement a very precise computation of the intrinsic viscosity for rigid molecules of arbitrary shape. The formulation, included in our program BEST, is tested against the analytical Simha formula for ellipsoids of revolution, and the results are essentially numerically exact. Previously unavailable, very precise results for a series of Platonic solids are also presented. The formulation includes the optional determination of the center of viscosity; however, for globular proteins, the difference compared to the computation based on the centroid is insignificant. The main application is to a series of 30 proteins ranging in molecular weight from 12 to 465 kD. The computation starts from the crystal structure as obtained from the Protein Data Bank, and a hydration thickness of 1.1 Å obtained in previous work with BEST was used. The results (extrapolated to an infinite number of triangular boundary elements) for the proteins are separated into two groups: monomeric and multimeric proteins. The agreement with experimental measurements of the intrinsic viscosity in the case of monomeric proteins is excellent and within experimental error of 5%, demonstrating that the solution and crystal structure are hydrodynamically equivalent. However, for some multimeric proteins, we observe strong systematic deviations around -20%, which we interpret as a systematic deviation of the solution structure from the crystal structure. A possible description of the structural change is deduced by using simple ellipsoid model parameters. A method to obtain intrinsic viscosity values for proteins to 1-2% accuracy (better than experimental error) on the basis of a single BE computation (avoiding the need for an extrapolation on the number of surface triangles) is also presented.
Collapse
Affiliation(s)
- David K Hahn
- Department of Chemistry and Biochemistry, San Francisco State University, 1600 Holloway Ave., San Francisco, California 94132
| | - Sergio R Aragon
- Department of Chemistry and Biochemistry, San Francisco State University, 1600 Holloway Ave., San Francisco, California 94132
| |
Collapse
|
8
|
Rocco M, Byron O. Computing translational diffusion and sedimentation coefficients: an evaluation of experimental data and programs. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2015; 44:417-31. [DOI: 10.1007/s00249-015-1042-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 05/04/2015] [Accepted: 05/13/2015] [Indexed: 11/28/2022]
|
9
|
Schermann SM, Simmons DA, Konermann L. Mass spectrometry-based approaches to protein–ligand interactions. Expert Rev Proteomics 2014; 2:475-85. [PMID: 16097882 DOI: 10.1586/14789450.2.4.475] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
One of the greatest current challenges in proteomics is to develop an understanding of cellular communication and regulation processes, most of which involve noncovalent interactions of proteins with various binding partners. Mass spectrometry plays an important role in all aspects of these research efforts. This article provides a survey of mass spectrometry-based approaches for exploring protein-ligand interactions. A wide array of techniques is available, and the choice of method depends on the specific problem at hand. For example, the high-throughput screening of compound libraries for binding to a specific receptor requires different approaches than structural studies on multiprotein complexes. This review is directed to readers wishing to obtain a concise yet comprehensive overview of existing experimental techniques. Specific emphasis is placed on emerging methods that have been developed within the last few years.
Collapse
Affiliation(s)
- Sonya M Schermann
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.
| | | | | |
Collapse
|
10
|
Wu ZQ, Jia WZ, Wang K, Xu JJ, Chen HY, Xia XH. Exploration of Two-Enzyme Coupled Catalysis System Using Scanning Electrochemical Microscopy. Anal Chem 2012. [DOI: 10.1021/ac3030224] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Zeng-Qiang Wu
- State Key Laboratory of Analytical Chemistry
for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210093, China
| | - Wen-Zhi Jia
- State Key Laboratory of Analytical Chemistry
for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210093, China
| | - Kang Wang
- State Key Laboratory of Analytical Chemistry
for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210093, China
| | - Jing-Juan Xu
- State Key Laboratory of Analytical Chemistry
for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210093, China
| | - Hong-Yuan Chen
- State Key Laboratory of Analytical Chemistry
for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210093, China
| | - Xing-Hua Xia
- State Key Laboratory of Analytical Chemistry
for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210093, China
| |
Collapse
|
11
|
Schug KA, Serrano C, Frycák P. Controlled band dispersion for quantitative binding determination and analysis with electrospray ionization-mass spectrometry. MASS SPECTROMETRY REVIEWS 2010; 29:806-829. [PMID: 19890977 DOI: 10.1002/mas.20267] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
This review discusses recent emerging techniques that have been used to couple flow-injection analysis (FIA) and electrospray ionization-mass spectrometry (ESI-MS) for the quantitation of noncovalent binding interactions. Focus is placed predominantly on two such methods. Diffusion-based measurements, developed by Konermann and co-workers, uses controlled-band dispersion prior to ESI-MS to determine diffusion constants and binding constants based on the temporal variation of ligand signal measured in the mass spectrum (an indirect technique). Dynamic titration, developed by Schug and co-workers, is a direct method, where a temporal compositional gradient of a guest molecule is induced in the presence of host in solution to monitor the concentration dependence of complex formation as a function of observed complex ion abundance after ESI-MS. Further discussion places these techniques in the context of a variety of other direct and indirect ESI-MS-based binding determination methods, and highlights advantages, disadvantages, and practical considerations for their proper use to investigate a broad range of macromolecular and small-molecule interaction systems.
Collapse
Affiliation(s)
- Kevin A Schug
- Department of Chemistry & Biochemistry, The University of Texas at Arlington, Arlington, Texas 76019-0065, USA.
| | | | | |
Collapse
|
12
|
Bielejewska A, Bylina A, Duszczyk K, Fiałkowski M, Hołyst R. Evaluation of Ligand-Selector Interaction from Effective Diffusion Coefficient. Anal Chem 2010; 82:5463-9. [DOI: 10.1021/ac1008207] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Anna Bielejewska
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland, and WMP-College of Science, UKSW, Dewajtis 5, Warsaw, Poland
| | - Andrzej Bylina
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland, and WMP-College of Science, UKSW, Dewajtis 5, Warsaw, Poland
| | - Kazimiera Duszczyk
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland, and WMP-College of Science, UKSW, Dewajtis 5, Warsaw, Poland
| | - Marcin Fiałkowski
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland, and WMP-College of Science, UKSW, Dewajtis 5, Warsaw, Poland
| | - Robert Hołyst
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland, and WMP-College of Science, UKSW, Dewajtis 5, Warsaw, Poland
| |
Collapse
|
13
|
Kelly R, Page J, Marginean I, Tang K, Smith R. Dilution-Free Analysis from Picoliter Droplets by Nano-Electrospray Ionization Mass Spectrometry. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200902501] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
14
|
Kaiser TJ, Thompson JW, Mellors JS, Jorgenson JW. Capillary-Based Instrument for the Simultaneous Measurement of Solution Viscosity and Solute Diffusion Coefficient at Pressures up to 2000 bar and Implications for Ultrahigh Pressure Liquid Chromatography. Anal Chem 2009; 81:2860-8. [DOI: 10.1021/ac802467k] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Theodore J. Kaiser
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
| | - J. Will Thompson
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
| | - J. Scott Mellors
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
| | - James W. Jorgenson
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
| |
Collapse
|
15
|
Kelly RT, Page JS, Marginean I, Tang K, Smith RD. Dilution-free analysis from picoliter droplets by nano-electrospray ionization mass spectrometry. Angew Chem Int Ed Engl 2009; 48:6832-5. [PMID: 19688798 PMCID: PMC2957286 DOI: 10.1002/anie.200902501] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Ryan T Kelly
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, WA 99352, USA.
| | | | | | | | | |
Collapse
|
16
|
Annis A, Chuang C, Nazef N. ALIS: An Affinity Selection–Mass Spectrometry System for the Discovery and Characterization of Protein–Ligand Interactions. ACTA ACUST UNITED AC 2007. [DOI: 10.1002/9783527610907.ch3] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
17
|
Wilson DJ, Konermann L. Ultrarapid desalting of protein solutions for electrospray mass spectrometry in a microchannel laminar flow device. Anal Chem 2007; 77:6887-94. [PMID: 16255586 DOI: 10.1021/ac050902o] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The adverse effects of nonvolatile salts on the electrospray (ESI) mass spectra of proteins and other biological analytes are a major obstacle for a wide range of applications. Numerous sample cleanup approaches have been devised to facilitate ESI-MS analyses. Recently developed microdialysis techniques can shorten desalting times down to several minutes, the bottleneck being diffusion of the contaminant through a semipermeable membrane. This work introduces an approach that allows the on-line desalting of macromolecule solutions within tens of milliseconds. The device does not employ a membrane; instead, it uses a two-layered laminar flow geometry that exploits the differential diffusion of macromolecular analytes and low molecular weight contaminants. To maximize desalting efficiency, diffusive exchange between the flow layers is permitted only for such a time as to allow full exchange of salt, while incurring minimal macromolecule exchange. Computer simulations and optical studies show that the device can reduce the salt concentration by roughly 1 order of magnitude, while retaining approximately 70% of the original protein concentration. Application of this approach to the on-line purification of salt-contaminated protein solutions in ESI-MS results in dramatic improvements of both the signal-to-noise ratio and the absolute signal intensity. However, efficient desalting requires the diffusion coefficients of salt and analyte to differ by roughly 1 order of magnitude or more. This technique has potential to facilitate high-throughput analyses of biological macromolecules directly from complex matrixes. In addition, it may become a valuable tool for process monitoring and for on-line kinetic studies on biological systems.
Collapse
Affiliation(s)
- Derek J Wilson
- Department of Chemistry, The University of Western Ontario, London, ON N6A 5B7, Canada
| | | |
Collapse
|
18
|
Aragon S, Hahn DK. Precise boundary element computation of protein transport properties: Diffusion tensors, specific volume, and hydration. Biophys J 2006; 91:1591-603. [PMID: 16714342 PMCID: PMC1544285 DOI: 10.1529/biophysj.105.078188] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2005] [Accepted: 03/24/2006] [Indexed: 11/18/2022] Open
Abstract
A precise boundary element method for the computation of hydrodynamic properties has been applied to the study of a large suite of 41 soluble proteins ranging from 6.5 to 377 kDa in molecular mass. A hydrodynamic model consisting of a rigid protein excluded volume, obtained from crystallographic coordinates, surrounded by a uniform hydration thickness has been found to yield properties in excellent agreement with experiment. The hydration thickness was determined to be delta = 1.1 +/- 0.1 A. Using this value, standard deviations from experimental measurements are: 2% for the specific volume; 2% for the translational diffusion coefficient, and 6% for the rotational diffusion coefficient. These deviations are comparable to experimental errors in these properties. The precision of the boundary element method allows the unified description of all of these properties with a single hydration parameter, thus far not achieved with other methods. An approximate method for computing transport properties with a statistical precision of 1% or better (compared to 0.1-0.2% for the full computation) is also presented. We have also estimated the total amount of hydration water with a typical -9% deviation from experiment in the case of monomeric proteins. Both the water of hydration and the more precise translational diffusion data hint that some multimeric proteins may not have the same solution structure as that in the crystal because the deviations are systematic and larger than in the monomeric case. On the other hand, the data for monomeric proteins conclusively show that there is no difference in the protein structure going from the crystal into solution.
Collapse
Affiliation(s)
- Sergio Aragon
- Department of Chemistry & Biochemistry, San Francisco State University, San Francisco, California, USA.
| | | |
Collapse
|
19
|
Ochran RA, Konermann L. Effects of ground loop currents on signal intensities in electrospray mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2004; 15:1748-1754. [PMID: 15589752 DOI: 10.1016/j.jasms.2004.08.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2004] [Revised: 08/04/2004] [Accepted: 08/05/2004] [Indexed: 05/24/2023]
Abstract
The occurrence of electrochemical processes during the operation of an electrospray ionization (ESI) source is well established. In the positive ion mode, electrons are drawn from the ESI metal capillary to a high voltage power supply. These electrons are the product of charge-balancing oxidation reactions taking place at the liquid/metal interface of the ion source. In a recent study, (Anal. Chem.2001, 73, 4836-4844), our group has shown that the introduction of a ground loop can dramatically enhance the rate of these oxidation processes. Such a ground loop can be introduced by connecting the sample infusion syringe (or the liquid chromatography column, in the case of LC-MS studies) to ground. The magnitude of the ground loop current can be controlled by the electrolyte concentration in the analyte solution, and by the dimensions of the capillary connecting the syringe needle and the ESI source. Using ferrocene as a model system, it is demonstrated that the introduction of such a ground loop can significantly enhance the signal intensity of analytes that form electrochemically ionized species during ESI. However, analytes that form protonated molecular ions, such as reserpine, also show higher signal intensities when a ground loop is introduced into the system. This latter observation is attributed to the occurrence of electrolytic solvent (acetonitrile and/or water) oxidation processes. These reactions generate protons within the ion source, and thus facilitate the formation of [M + nH](n+) ions. Overall, this work provides an example of how the careful control of electrochemical parameters can be exploited to optimize signal intensities in ESI-MS.
Collapse
Affiliation(s)
- Richard A Ochran
- Department of Chemistry, The University of Western Ontario, London, ON N6A 5B7, Canada
| | | |
Collapse
|
20
|
Konermann L. 2003 Fred Beamish Award Lecture Exploring the dynamics of biological systems by mass spectrometry. CAN J CHEM 2004. [DOI: 10.1139/v04-132] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
This review describes the use of electrospray ionization mass spectrometry (ESI-MS) in conjunction with on-line rapid mixing techniques. This combination, termed "time-resolved" ESI-MS, provides a powerful approach for studying solution-phase reactions on timescales as short as a few milliseconds. Of particular interest is the application of this technique for monitoring protein folding reactions. Time-resolved ESI-MS can provide detailed information on structural changes of the polypeptide chain, while at the same time probing the occurrence of noncovalent ligandprotein interactions. Especially when used in combination with hydrogendeuterium pulse labeling, these measurements yield valuable structural information on short-lived folding intermediates. Similar approaches can be used to monitor the dynamics of proteins under equilibrium conditions. Another important application of time-resolved ESI-MS are mechanistic studies on enzyme-catalyzed processes. These reactions can be monitored under presteady-state conditions, without requiring artificial chromophoric substrates or radioactive labeling. We also discuss the use of ESI-MS for monitoring noncovalent ligandprotein interactions by diffusion measurements. In contrast to conventional MS-based techniques, this approach does not rely on the preservation of noncovalent interactions in the gas phase. It appears that diffusion measurements by ESI-MS could become an interesting alternative to existing methods for the high throughput screening of compound libraries in the context of drug discovery.Key words: reaction intermediate, rapid mixing, kinetics, protein conformation, protein function.
Collapse
|
21
|
Clark SM, Konermann L. Determination of Ligand−Protein Dissociation Constants by Electrospray Mass Spectrometry-Based Diffusion Measurements. Anal Chem 2004; 76:7077-83. [PMID: 15571362 DOI: 10.1021/ac049344o] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A novel approach for the quantification of ligand-protein interactions is presented. Electrospray ionization mass spectrometry (ESI-MS) is used to monitor the diffusion behavior of noncovalent ligands in the presence of their protein receptors. These data allow the fraction of free ligand in solution to be determined, such that the corresponding dissociation constants can be calculated. A set of conditions is developed that provides an "allowable range" of concentrations for this type of assay. The method is tested by applying it to two different inhibitor-enzyme systems. The dissociation constants measured for benzamidine-trypsin and for N,N',N' '-triacetylchitotriose-lysozyme are (50 +/- 10) and (6 +/- 1) mM, respectively. Both of these results are in good agreement with previous data from the literature. In contrast to traditional ESI-MS-based methods, the approach used in this work does not rely on the preservation of specific solution-type noncovalent interactions in the gas phase. It is shown that this method allows an accurate determination of dissociation constants, even in cases in which the ion abundance ratio of free to ligand-bound protein in ESI-MS does not reflect the corresponding concentration ratio in solution.
Collapse
Affiliation(s)
- Sonya M Clark
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | | |
Collapse
|
22
|
Clark SM, Konermann L. Screening for Noncovalent Ligand−Receptor Interactions by Electrospray Ionization Mass Spectrometry-Based Diffusion Measurements. Anal Chem 2004; 76:1257-63. [PMID: 14987079 DOI: 10.1021/ac035230l] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The application of a novel method for the identification of low-molecular-weight noncovalent ligands to a macromolecular target is reported. This technique is based on the measurement of analyte diffusion coefficients by electrospray mass spectrometry (ESI-MS) (Clark et al., Rapid Commun. Mass Spectrom. 2002, 16, 1454-1462). Potential ligands have large diffusion coefficients as long as they are free in solution. Binding to a macromolecular target, however, drastically reduces the diffusional mobility of any ligand species. Mixtures containing six different saccharides [ribose, rhamnose, glucose, maltose, maltotriose, and N,N',N''-triacetylchitotriose (NAG(3))] were screened for noncovalent binding to lysozyme. Of these six compounds, only NAG(3) is known to bind to the protein. In "direct" binding tests, NAG(3) shows a significantly reduced diffusion coefficient in the presence of the protein. No changes were observed for any of the other saccharides. In a second set of experiments, the use of a "competition" screening method was explored in which mixtures of candidate saccharides were tested for their ability to displace a reference ligand from the target. The addition of NAG(3)-containing mixtures significantly increased the diffusion coefficient of the reference ligand NAG(4) (N,N',N'',N'''-tetraacetylchitotetrose), whereas mixtures that did not contain NAG(3) had no effect. These data clearly indicate the potential of ESI-MS-based diffusion measurements as a novel tool to screen compound libraries for binding to proteins and other macromolecular targets. In contrast to conventional ESI-MS-based ligand-receptor binding studies, this method does not rely on the preservation of noncovalent interactions in the gas phase.
Collapse
Affiliation(s)
- Sonya M Clark
- Department of Chemistry, The University of Western Ontario, London, Ontario, N6A 5B7, Canada
| | | |
Collapse
|
23
|
Clark SM, Konermann L. Diffusion measurements by electrospray mass spectrometry for studying solution-phase noncovalent interactions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2003; 14:430-441. [PMID: 12745212 DOI: 10.1016/s1044-0305(03)00123-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
This study describes a novel approach for monitoring noncovalent interactions in solution by electrospray mass spectrometry (ESI-MS). The technique is based on measurements of analyte diffusion in solution. Diffusion coefficients of a target macromolecule and a potential low molecular weight binding partner are determined by measuring the spread of an initially sharp boundary between two solutions of different concentration in a laminar flow tube (Taylor dispersion), as described in Rapid Commun. Mass Spectrom. 2002, 16, 1454-1462. In the absence of noncovalent interactions, the measured ESI-MS dispersion profiles are expected to show a gradual transition for the macromolecule and a steep transition for the low molecular weight compound. However, if the two analytes form a noncovalent complex in solution the dispersion profiles of the two species will be very similar, since the translational diffusion of the small compound is determined by the slow Brownian motion of the macromolecule. In contrast to conventional ESI-MS-based techniques for studying noncovalent complexes, this approach does not rely on the preservation of solution-phase interactions in the gas phase. On the contrary, "harsh" conditions at the ion source are required to disrupt any potential gas- phase interactions between the two species, such that their dispersion profiles can be monitored separately. The viability of this technique is demonstrated in studies on noncovalent heme-protein interactions in myoglobin. Tight noncovalent binding is observed in solutions of pH 10, both in the absence and in the presence of 30% acetonitrile. In contrast, a significant disruption of the noncovalent interactions is seen at an acetonitrile content of 50%. Under these conditions, the diffusion coefficient of heme in the presence of myoglobin is only slightly lower than that of heme in a protein-free solution. A breakdown of the noncovalent interactions is also observed in aqueous solution of pH 2.4, where myoglobin is known to adopt an acid-unfolded conformation.
Collapse
Affiliation(s)
- Sonya M Clark
- Department of Chemistry, The University of Western Ontario, London, Ontario, Canada
| | | |
Collapse
|
24
|
Current literature in mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2002; 37:1176-1184. [PMID: 12447897 DOI: 10.1002/jms.258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
|